I have a Phonegap App (Flapcast Mobile) that I think works quite well; The only thing that makes it feel like its not native is because I did the art and design myself and I'm not very good at that. There are plenty of (native) apps that don't use native UI controls, its just up to you to make it look and feel good.

My advice is to stay away from the UI libraries, they don't actually look that good and are slow and clunky. Just roll your own if you can, or find a lightweight UI library. But do use a JS framework; I used Backbone.js and it runs like a charm; LinkedIn also wrote a mobile app with Backbone.js (they may have gone native recently though?) and it was beautiful.